Contacts of the helix formed by residues 230 - 246 (chain B) in PDB entry 3QNQ
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with SER 230 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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226B ILE 3.3 8.1 + - - -
227B LEU* 3.0 26.0 - - - -
228B GLY 3.0 1.7 - - - +
229B ALA* 1.3 85.5 - - - +
231B LEU* 1.3 65.4 + - - +
232B TRP* 3.1 18.9 + - - +
233B GLY 3.3 7.2 + - - -
234B ALA* 3.2 22.3 + - - +
284B ILE* 4.0 2.1 - - - +
364B TYR* 4.7 0.9 - - - -
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Residues in contact with LEU 231 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229B ALA 3.8 0.2 + - - -
230B SER* 1.3 72.5 + - - +
232B TRP* 1.3 64.2 + - + +
233B GLY 3.1 0.2 - - - -
234B ALA* 3.3 1.7 + - + -
235B VAL* 2.9 40.9 + - + +
360B THR* 4.6 8.1 - - + -
361B ILE* 4.9 13.5 - - + -
364B TYR* 3.4 63.0 + - + +
365B PHE* 3.9 20.4 - - + -
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Residues in contact with TRP 232 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230B SER* 3.1 10.6 + - - +
231B LEU* 1.3 81.9 - - + +
233B GLY* 1.3 56.5 + - - +
235B VAL* 3.9 17.9 - - + -
236B ILE* 2.9 64.4 + - + +
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Residues in contact with GLY 233 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227B LEU 3.4 22.0 - - - -
228B GLY* 4.0 8.3 - - - -
230B SER* 3.3 11.5 - - - -
231B LEU 3.1 1.0 - - - -
232B TRP* 1.3 79.6 - - - +
234B ALA* 1.3 59.0 + - - +
236B ILE* 4.6 1.9 - - - +
237B ALA* 3.3 24.6 + - - +
259B MET* 4.9 7.1 - - - +
263B TRP* 5.0 0.9 - - - -
289B PHE* 5.5 0.2 - - - -
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Residues in contact with ALA 234 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228B GLY 4.2 1.0 + - - -
230B SER 3.2 9.1 + - - +
231B LEU* 3.3 5.6 + - + +
233B GLY* 1.3 74.4 - - - +
235B VAL* 1.3 64.4 + - - +
238B VAL* 3.2 30.0 + - - +
284B ILE* 3.6 34.3 - - + -
288B PHE* 4.3 0.4 - - + -
289B PHE* 3.6 22.0 - - + -
360B THR* 4.0 16.3 - - + +
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Residues in contact with VAL 235 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231B LEU* 2.9 25.5 + - + +
232B TRP* 4.2 25.4 - - + +
234B ALA* 1.3 74.7 - - - +
236B ILE* 1.3 59.1 + - + +
238B VAL* 3.0 5.7 + - - +
239B ILE* 2.7 54.5 + - + +
357B VAL* 5.1 9.4 - - + +
360B THR* 4.2 18.8 - - + -
361B ILE* 4.3 21.5 - - + -
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Residues in contact with ILE 236 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232B TRP* 2.9 52.9 + - + +
233B GLY* 4.6 2.0 - - - +
235B VAL* 1.3 76.1 - - + +
237B ALA* 1.3 58.3 + - - +
239B ILE* 3.9 5.4 - - - +
240B LEU* 3.1 38.7 + - + +
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Residues in contact with ALA 237 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233B GLY 3.3 20.0 + - - +
234B ALA* 4.0 4.0 - - - +
235B VAL 3.1 0.8 - - - -
236B ILE* 1.3 75.6 - - - +
238B VAL* 1.3 54.8 + - - +
240B LEU* 3.1 7.1 + - - +
241B VAL* 2.7 40.6 + - - +
255B VAL* 4.2 7.3 - - + +
259B MET* 5.0 4.7 - - + -
263B TRP* 3.5 36.1 - - + -
289B PHE* 5.0 1.8 - - + -
294B TYR* 5.7 0.2 - - - +
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Residues in contact with VAL 238 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234B ALA 3.2 17.8 + - - +
235B VAL* 3.0 5.3 + - - +
237B ALA* 1.3 78.2 - - - +
239B ILE* 1.3 62.5 + - - +
241B VAL* 3.4 0.4 + - - -
242B HIS* 3.0 29.8 + - + -
289B PHE* 3.6 22.9 - - + -
293B ILE* 4.3 2.0 - - + -
294B TYR* 3.8 21.3 - - + +
353B ILE 5.4 0.4 - - - +
356B PRO* 3.4 40.6 - - + -
357B VAL* 4.2 7.4 - - + +
360B THR* 3.5 16.4 - - - +
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Residues in contact with ILE 239 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235B VAL* 2.7 37.0 + - + +
236B ILE* 4.2 6.3 - - - +
238B VAL* 1.3 70.5 - - - +
240B LEU* 1.3 65.6 + - + +
242B HIS* 4.5 2.4 - - - -
243B VAL* 3.3 36.6 + - + +
353B ILE* 4.9 11.7 - - + -
357B VAL* 3.4 33.9 - - + -
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Residues in contact with LEU 240 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236B ILE* 3.1 30.6 + - + +
237B ALA* 3.1 5.7 + - - +
239B ILE* 1.3 79.5 - - + +
241B VAL* 1.3 66.4 + - - +
242B HIS 3.0 3.6 + - - -
243B VAL* 3.4 14.6 + - + +
244B LEU* 3.2 32.0 + - + +
255B VAL* 3.7 20.6 - - + -
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Residues in contact with VAL 241 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237B ALA* 2.7 24.8 + - + +
238B VAL 3.6 2.0 - - - +
240B LEU* 1.3 72.6 - - - +
242B HIS* 1.3 80.3 + - + +
245B TRP* 3.0 21.0 + - + -
251B GLY* 3.4 19.0 - - - +
252B ALA* 3.7 22.0 - - - +
255B VAL* 3.5 28.7 - - + -
256B GLY 5.0 0.9 - - - +
263B TRP* 5.3 1.3 - - + -
294B TYR* 3.5 21.3 - - + +
2G NAG 4.1 9.2 - - + -
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Residues in contact with HIS 242 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238B VAL* 3.0 20.7 + - + +
239B ILE 4.6 1.6 - - - +
240B LEU 3.0 0.8 - - - -
241B VAL* 1.3 99.6 + - + +
243B VAL* 1.3 58.1 + - - +
244B LEU 2.9 5.2 - - - -
245B TRP* 3.2 8.5 + + - +
246B ALA* 2.9 25.1 + - - +
294B TYR* 3.6 23.5 - + - -
298B SER* 2.5 31.9 + - - -
352B PHE* 3.4 24.2 - + + +
353B ILE* 4.5 15.4 - - + +
356B PRO* 3.1 34.6 - - + +
2G NAG 4.5 1.1 - - + -
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Residues in contact with VAL 243 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B VAL* 3.7 22.5 - - + +
239B ILE* 3.3 28.2 + - + +
240B LEU* 3.9 20.4 - - + +
242B HIS* 1.3 74.0 - - - +
244B LEU* 1.3 58.8 + - + +
246B ALA* 3.8 13.7 - - + +
247B CYS* 3.6 18.9 - - - -
353B ILE* 3.5 32.5 - - + -
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Residues in contact with LEU 244 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B VAL* 4.9 4.5 - - + -
13B ALA* 3.3 37.0 - - + +
16B VAL* 5.9 1.6 - - + -
240B LEU* 3.2 21.6 + - + +
241B VAL 4.0 0.2 - - - +
242B HIS 2.9 0.6 - - - -
243B VAL* 1.3 85.8 - - + +
245B TRP* 1.3 65.7 + - - +
246B ALA 3.0 0.9 - - - -
247B CYS* 2.9 14.8 + - - +
248B GLY 3.3 0.2 + - - -
249B ILE* 3.0 27.9 + - + +
251B GLY* 3.7 24.7 - - - +
254B ILE* 3.6 33.4 - - + -
255B VAL* 4.8 7.9 - - + -
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Residues in contact with TRP 245 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241B VAL* 3.0 26.2 + - + -
242B HIS* 3.2 11.1 + - - +
244B LEU* 1.3 78.0 - - - +
246B ALA* 1.3 55.7 + - - +
248B GLY* 2.6 23.8 + - - -
249B ILE 3.0 24.0 + - - -
250B HIS* 3.2 42.4 - + + -
251B GLY 3.8 8.6 - - - +
252B ALA 3.8 2.6 - - - +
298B SER* 3.8 15.0 - - - -
333B ASN* 4.8 1.3 - - - -
334B GLU* 3.5 16.2 - - - -
337B THR* 3.8 20.4 - - - -
338B PHE* 3.5 31.9 - + - -
343B VAL* 3.6 14.9 - - + +
352B PHE* 3.7 18.4 - + + -
2G NAG 2.7 35.8 + - - -
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Residues in contact with ALA 246 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242B HIS 2.9 14.8 + - - +
243B VAL* 3.8 18.2 - - + +
245B TRP* 1.3 78.4 - - - +
247B CYS* 1.3 60.1 + - - +
248B GLY 3.4 2.1 + - - -
343B VAL* 3.6 1.3 - - - +
344B MET* 2.9 34.3 + - - +
349B LEU* 3.7 36.8 - - + -
353B ILE* 5.3 2.9 - - + -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il